Hi, I have owned my ipad1 since it was available for sell. My iPad 1 still runs perfectly. Now I am debating whether I should upgrade it to iPad 2 or ipad3, or simply keep using iPad1 until ipad4 becomes available. I use iPad for reading pdf documents (scientific papers) (no movies, games, etc.). Is it worth to buy a new iPad? If yes, should I get an ipad2 or iPad 3. By reading the previous posts in the forum, I found ipad3 has problems of overheating and short battery life. Is that really true even for reading PDF documents? Would iPad 3 hurt my eyes less for long time reading than iPad 1/2? Thanks for any advice.

No, it doesn't have such problems.
There were overheating reports at launch which all seem to track back to the same original story, which said that it ran hotter than the iPad 2, not that it an actual issue with failing due to overheating. The rest is just FUD.
I find the battery life to be similar to the iPad 1.
For just reading, I don't see a huge advantage in switching from 1 to 2, unless you have complex documents that the better processor in the 2 would render more quickly.
The 3 adds a much higher resolution screen, and would certainly be nicer to read on than the 1, but whether that is worth of the cost of upgrading is hard for someone else to say for you.
Best bet is to pop into an Apple store and have a play with one.